TLR5: Toll-like receptor 5 Kavita Athalye, Sabrina Madni, Ashley Graham
This project:
This web page originated as an assignment in Emory University's Biology 142 lab course. Students were assigned proteins of interest and asked to research what is known about the protein and to examine whether the newly sequenced whale shark genome had evidence of an orthologous protein. This specific Wiki page addresses TLR5.
Background information:
Vertebrate immune systems are composed of both innate and acquired immunity. The innate immunity system is able to recognize PAMPs, or pathogen associated molecular patterns by TLRs (toll-like receptors), which are present on the surface of immune cells [1]. TLRs are a type 1 transmembrane protein, and are part of the host's defense mechanism against the growth and spread of bacteria [1].
TLR5 can recognize bacterial flagellin, which is a virulence factor [5]. On recognition, the receptor mediates tumor necrosis factor-alpha production [5]. In humans, TLR5 is expressed in monocytes, polymorphonuclear leukocytes, and dendritic cells [9]. TLR5 is expressed on the surface of cells and can recognize the lipids, lipoproteins, and proteins of microbial membranes [2].
Figure 1. Part (A) shows the structure of TLR5.
Methods:
The FASTA sequence of TLR5 was obtained through Ensembl [4] using its ID (ENSP00000440643). The Georgia Aquarium Galaxy Server[6] was then utilized to run a protein BLAST of the human protein sequence for TLR5, as the query, against the predicted whale shark protein database. The FASTA sequence was extracted for the top five chosen proteins. Each FASTA sequence was then BLASTed against the NCBI human protein database[3] to find the best match. The human sequence was then blasted against the mouse, zebra fish, yeast, clawed frog, dog, and elephant shark using the NCBI protein database to check for similarities across species. The FASTA sequences were extracted and Clustlaw[7] was used to form a phylogenic tree.
Whale shark protein research:
Figures 2, 3, 4, and 5 highlight the best whale shark genome sequences which were to be blasted against the human genome to see which is most closely related to the TLR5 protein in humans. The highlighted sequences were chosen based on the most favorable combination of lowest e-value and percent value. As can be seen, there were many sequences which were returned.
Figure 2. Data from blasting human TLR5 protein against the whale shark genome. The first section of the results contains two of the five results which were chosen to be furthered blasted against the human genome. The highlighted sequences have a low e-value and an adequate percent identity.
Figure 3. Data from blasting human TLR5 protein against the whale shark genome. The second section of results shows one of the five results which were chosen to be furthered blasted against the human genome. The highlighted sequence has a low e-value and an adequate percent identity.
Figure 4. Data from blasting human TLR5 protein against the whale shark genome. The third section of results shows one of the five results which were chosen to be furthered blasted against the human genome. The highlighted sequence has a low e-value and an adequate percent identity.
Figure 5. Data from blasting human TLR5 protein against the whale shark genome. The third section of results shows one of the five results which were chosen to be furthered blasted against the human genome. The highlighted sequence has a low e-value and an adequate percent identity.
Protein Domain:
The most likely ortholog in the whale shark protein database is toll-like receptor 5 precursor which is the same in human beings and other species such as dog, zebra fish, mouse, and clawed frog. TLR5 is part of the toll receptor family; toll receptors are a type 1 transmembrane protein consisting of three major domains and characterized by LRRs (leucine rich repeats) which allows them to recognize PAMP [2]. Toll receptors are conserved through evolution, with their homologs found in insects, plants and mammals [1].
Comparing species: Orthologs
The human protein sequence for TLR5 was BLASTed against the genomes of whale shark, mouse, elephant shark, dog, clawed frog, zebra fish, and yeast to see if there were any orthologs. As can be seen in Fig.6 , in the whale shark, mouse, dog, clawed frog, and zebra fish, orthologs for toll-like receptor 5 precursor were found, suggesting that these species all have the same protein TLR5 and are related. Note however, that these are precursors. Also, the type of toll-receptor in zebra fish is 5b. In the elephant shark, a predicted toll-like receptor 3 was found, which correlates to the elephant shark being the most similar species known to the whale shark.
Figure 6. Protein sequence information for the top five matching whale shark sequences as well as the most closely related protein sequences from a mouse, zebra fish, yeast, clawed frog, dog, and elephant shark when blasted against the human protein sequence for TLR5 were compiled into a table.
Figure 7. A phylogenetic tree was compiled based upon the protein sequences for the most closely related protein to TLR5 in each of the researched species.
Conclusion:
The human toll-like receptor 5 in its precursor form was found in the genomes of whale shark, mouse, elephant shark, dog, clawed frog, and zebra fish. No similar protein sequence was found in yeast. This data is supported by the phylogenetic tree in Fig. 7, which shows that the species with toll-like receptor 5 are separated from the yeast by a divergence from a common ancestor. The yeast may have lost the gene at this initial divergence. Further, this could suggest that these species with toll-like receptor 5 are closely related in terms of their immune system response to bacterial flagellin. It can be seen that the whale shark and elephant shark are closely related, with the whale shark having toll-like receptor 5 precursor and the elephant shark having a predicted toll-like receptor 3. TLR3 is thought to be involved in viral recognition [1]; it can sense foreign nucleic acids and stimulate the anti-viral innate immune response through the production of type 1 IFN and inflammatory cytokines [2]. Therefore, this could suggest that the protein sequence in whale shark functions to defend the host from bacterial infections while in the elephant shark, the protein sequence functions to defend the host from viral infections.
Data about TLRs in chondrichthyes is not abundant, however the little data that is available does confirm the presence of TLRs in sharks [10]. TLRs in whale sharks could be researched into further to examine similarities across species with regards to immune response, in particular, response to bacterial flagellin.
5. Fumitaka Hayashi, Kelly D. Smith, Adrian Ozinsky, Thomas R. Hawn, Eugene C. Yi, David R. Goodlett, Jimmy K. Eng, Shizuo Akira, David M. Underhill and Alan Aderem. "The Innate Immune Response to Bacterial Flagellin Is Mediated by Toll-like Receptor 5." Nature (2001): 1099-1103. Web. 07 Apr. 2015.<http://www.nature.com/nature/journal/v410/n6832/full/4101099a0.html>
9. Muzio, Marta, Daniela Bosisio, Nadia Polentarutti, Giovanna D'amico, Antonella Stoppacciaro, Roberta Mancinelli, Cornelis Veer, Giselle Penton-Rol, Luigi Ruco, Paola Allavena, and Alberto Mantovani. "Differential Expression and Regulation of Toll-Like Receptors (TLR) in Human Leukocytes: Selective Expression of TLR3 in Dendritic Cells." The Journal of Immunology 164 (2000): 5998-6004. Web. 07 Apr. 2015. <http://www.jimmunol.org/content/164/11/5998.long>
TLR5
TLR5: Toll-like receptor 5
Kavita Athalye, Sabrina Madni, Ashley Graham
This project:
This web page originated as an assignment in Emory University's Biology 142 lab course. Students were assigned proteins of interest and asked to research what is known about the protein and to examine whether the newly sequenced whale shark genome had evidence of an orthologous protein. This specific Wiki page addresses TLR5.
Background information:
Vertebrate immune systems are composed of both innate and acquired immunity. The innate immunity system is able to recognize PAMPs, or pathogen associated molecular patterns by TLRs (toll-like receptors), which are present on the surface of immune cells [1]. TLRs are a type 1 transmembrane protein, and are part of the host's defense mechanism against the growth and spread of bacteria [1].
TLR5 can recognize bacterial flagellin, which is a virulence factor [5]. On recognition, the receptor mediates tumor necrosis factor-alpha production [5]. In humans, TLR5 is expressed in monocytes, polymorphonuclear leukocytes, and dendritic cells [9]. TLR5 is expressed on the surface of cells and can recognize the lipids, lipoproteins, and proteins of microbial membranes [2].
Figure 1. Part (A) shows the structure of TLR5.
Methods:
The FASTA sequence of TLR5 was obtained through Ensembl [4] using its ID (ENSP00000440643). The Georgia Aquarium Galaxy Server[6] was then utilized to run a protein BLAST of the human protein sequence for TLR5, as the query, against the predicted whale shark protein database. The FASTA sequence was extracted for the top five chosen proteins. Each FASTA sequence was then BLASTed against the NCBI human protein database[3] to find the best match. The human sequence was then blasted against the mouse, zebra fish, yeast, clawed frog, dog, and elephant shark using the NCBI protein database to check for similarities across species. The FASTA sequences were extracted and Clustlaw[7] was used to form a phylogenic tree.
Whale shark protein research:
Figures 2, 3, 4, and 5 highlight the best whale shark genome sequences which were to be blasted against the human genome to see which is most closely related to the TLR5 protein in humans. The highlighted sequences were chosen based on the most favorable combination of lowest e-value and percent value. As can be seen, there were many sequences which were returned.
Figure 2. Data from blasting human TLR5 protein against the whale shark genome. The first section of the results contains two of the five results which were chosen to be furthered blasted against the human genome. The highlighted sequences have a low e-value and an adequate percent identity.
Figure 3. Data from blasting human TLR5 protein against the whale shark genome. The second section of results shows one of the five results which were chosen to be furthered blasted against the human genome. The highlighted sequence has a low e-value and an adequate percent identity.
Figure 4. Data from blasting human TLR5 protein against the whale shark genome. The third section of results shows one of the five results which were chosen to be furthered blasted against the human genome. The highlighted sequence has a low e-value and an adequate percent identity.
Figure 5. Data from blasting human TLR5 protein against the whale shark genome. The third section of results shows one of the five results which were chosen to be furthered blasted against the human genome. The highlighted sequence has a low e-value and an adequate percent identity.
Protein Domain:
The most likely ortholog in the whale shark protein database is toll-like receptor 5 precursor which is the same in human beings and other species such as dog, zebra fish, mouse, and clawed frog. TLR5 is part of the toll receptor family; toll receptors are a type 1 transmembrane protein consisting of three major domains and characterized by LRRs (leucine rich repeats) which allows them to recognize PAMP [2]. Toll receptors are conserved through evolution, with their homologs found in insects, plants and mammals [1].
Comparing species: Orthologs
The human protein sequence for TLR5 was BLASTed against the genomes of whale shark, mouse, elephant shark, dog, clawed frog, zebra fish, and yeast to see if there were any orthologs. As can be seen in Fig.6 , in the whale shark, mouse, dog, clawed frog, and zebra fish, orthologs for toll-like receptor 5 precursor were found, suggesting that these species all have the same protein TLR5 and are related. Note however, that these are precursors. Also, the type of toll-receptor in zebra fish is 5b. In the elephant shark, a predicted toll-like receptor 3 was found, which correlates to the elephant shark being the most similar species known to the whale shark.
Figure 6. Protein sequence information for the top five matching whale shark sequences as well as the most closely related protein sequences from a mouse, zebra fish, yeast, clawed frog, dog, and elephant shark when blasted against the human protein sequence for TLR5 were compiled into a table.
Figure 7. A phylogenetic tree was compiled based upon the protein sequences for the most closely related protein to TLR5 in each of the researched species.
Conclusion:
The human toll-like receptor 5 in its precursor form was found in the genomes of whale shark, mouse, elephant shark, dog, clawed frog, and zebra fish. No similar protein sequence was found in yeast. This data is supported by the phylogenetic tree in Fig. 7, which shows that the species with toll-like receptor 5 are separated from the yeast by a divergence from a common ancestor. The yeast may have lost the gene at this initial divergence. Further, this could suggest that these species with toll-like receptor 5 are closely related in terms of their immune system response to bacterial flagellin. It can be seen that the whale shark and elephant shark are closely related, with the whale shark having toll-like receptor 5 precursor and the elephant shark having a predicted toll-like receptor 3. TLR3 is thought to be involved in viral recognition [1]; it can sense foreign nucleic acids and stimulate the anti-viral innate immune response through the production of type 1 IFN and inflammatory cytokines [2]. Therefore, this could suggest that the protein sequence in whale shark functions to defend the host from bacterial infections while in the elephant shark, the protein sequence functions to defend the host from viral infections.
Data about TLRs in chondrichthyes is not abundant, however the little data that is available does confirm the presence of TLRs in sharks [10]. TLRs in whale sharks could be researched into further to examine similarities across species with regards to immune response, in particular, response to bacterial flagellin.
References:
1. Akira, Shizuo, and Hiroaki Hemmi. "Recognition of Pathogen-associated Molecular Patterns by TLR Family." Immunology Letters 85.2 (2003): 85-95. Web. 07 Apr. 2015.<http://www.sciencedirect.com/science/article/pii/S0165247802002286>
2. Akira, Shizuo, and Kawai Taro. "The Roles of TLRs, RLRs and NLRs in Pathogen Recognition." Intl. Immunol. (2009): 317-337. Web. 07 Apr. 2015.
<http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2721684/>
3.
"Basic Local Alignment Search Tool." BLAST:. N.p., n.d. Web. <http://blast.ncbi.nlm.nih.gov/>.
4.
"Ensembl Genome Browser." Ensembl Genome Browser. N.p., n.d. Web. <http://ensembl.org/>.
5. Fumitaka Hayashi, Kelly D. Smith, Adrian Ozinsky, Thomas R. Hawn, Eugene C. Yi, David R. Goodlett, Jimmy K. Eng, Shizuo Akira, David M. Underhill and Alan Aderem. "The Innate Immune Response to Bacterial Flagellin Is Mediated by Toll-like Receptor 5." Nature (2001): 1099-1103. Web. 07 Apr. 2015.<http://www.nature.com/nature/journal/v410/n6832/full/4101099a0.html>
6.
"Galaxy / Whale Shark." Galaxy / Whale Shark. Georgia Aquarium, n.d. Web. <http://whaleshark.georgiaaquarium.org/>.
7.
"GenomeNet." GenomeNet. N.p., n.d. Web. <http://www.genome.jp/clustlaw>
8. image of TLR5 in Figure 1: http://www.sciencemag.org/content/335/6070/859/F2.large.jpg
9. Muzio, Marta, Daniela Bosisio, Nadia Polentarutti, Giovanna D'amico, Antonella Stoppacciaro, Roberta Mancinelli, Cornelis Veer, Giselle Penton-Rol, Luigi Ruco, Paola Allavena, and Alberto Mantovani. "Differential Expression and Regulation of Toll-Like Receptors (TLR) in Human Leukocytes: Selective Expression of TLR3 in Dendritic Cells." The Journal of Immunology 164 (2000): 5998-6004. Web. 07 Apr. 2015.
<http://www.jimmunol.org/content/164/11/5998.long>
10. Rauta, Pradipta, Mrinal Samanta, Hirak Dash, Bismita Nayak, and Surajit Das. "Toll-like Receptors (TLRs) in Aquatic Animals: Signaling Pathways, Expressions and Immune Responses." Immunology Letters 158.1-2 (2014): 14-24. Web. 07 Apr. 2015
<http://www.sciencedirect.com/science/article/pii/S0165247813001958>